Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private tutor. I am CC'ing your message to the list and would ask that all
further discussion be sent there. See comments below.
Yanping Fan, Liza (Dr) wrote:
Dear Justin:
Good day.
I found your comments in gmx-user communications. And you are very
experienced in GMX. I’m using gmx 453 now, with DNA system. Pdb2gmx is
ok, but gmx treated each string as protein. I used command
What do you mean "treated each string as protein?" DNA residues are defined in
residuetypes.dat as such, so I don't know how DNA residues would be interpreted
as protein by any tool. In principle, there is no problem with this
interpretation, as long as the parameters are assigned correctly.
The .pdb file you sent me contains both protein and DNA, so I suspect that
nothing is wrong; you have some residues that are DNA and others that are
protein. You don't say which tool is treating your DNA as protein, but I would
encourage you to check the output carefully. If you still suspect something is
wrong, please provide useful diagnostic information (i.e., the tool reporting
the potential problem and the output it is giving you that leads you to suspect
a problem).
pdb2gmx -f new.pdb -o wt.gro -p wt.top -water tip4p
then choose charmm27 ff,
everything looks good. However I found during my md runs, DNA separated.
System goes to weird. Do I need to remove TER between the paired stands?
I attached pdb file for your reference. Thank you very much for your
guildance.
There is probably not separation, just a periodicity effect.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
-Justin
Best regards,
Liza
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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